After some research we finally found the problem.

The classmap files were too big.
After splitting them into several smaller ones, we had a huge improve in
performance. 

So perhaps that could be an interesting point others could benefit from.

We indeed used APC, but the opcode cache was defeated by the size,
obviously.  

So either increasing the opcode cache or splitting the classmap files into
smaller ones could be the solution in such cases. 

So, like you mentioned, the opcode is really important in the context of
classmap autoloading, but one have to make sure that the files are actually
cached and not drop out because of some filesize limits. 

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